1Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, China.

Abstract

Thirty HIV-1 URF_01AE/ B' complete or nearly full-length genome sequences sampled within Southeast Asia were obtained from the Los Alamos HIV Sequence Database. Phylogenetic and recombinant analyses revealed that three sequences indeed displayed the identical recombinant structure. Of note, the three subjects, harboring novel CRF01_AE/B recombinants, did not have apparent epidemiological linkage. They fulfilled the criteria for the designation of a new circulating recombinant form (CRF) and constituted the 52nd CRF identified in the worldwide HIV-1 pandemic. In this chimera, two short subtype B segments were inserted into a backbone of CRF_01AE. The breakpoints corresponded to HXB2 nucleotide positions 2930, 3251, 8521, and 9004 approximately. This CRF is the first one identified by neatening and analyzing the sequences already presented in the Los Alamos HIV Sequence Database. This indicates that we should pay attention not only to explicit subtype sequences but also to those classified as a unique recombinant form (URF) so far.

Identification of a novel circulating recombinant form (CRF) candidate. The neighbor-joining phylogenetic tree is constructed based on the nucleotide sequence of nearly full-length genomes using MEGA 5.04. The tree is rooted with group O. All the reference strains were retrieved from the Los Alamos HIV Sequence Database. Values on the branches represent the percentage of 1000 bootstrap replicates and bootstrap values over 70% are shown in the tree. The novel CRF candidate is marked with a solid circle. The scale bar indicates 5% nucleotide sequence divergence.

Phylogenetic trees for genome segments of the novel identified CRF52_01B. The neighbor-joining tree is constructed using MEGA 5.04.Values at the nodes indicate the percent bootstraps in which the cluster to the right was supported. Bootstraps of 70% and higher only are shown. The scale bars are shown at the bottom. •=CRF52_01B; ▴=Thailand CRF01_AE; ▪=African CRF01_AE;▾=Thailand B; □=Western B.